Installation¶
Quick overview¶
For those users who have already read this page, and need a quick refresher (or prefer to act first, and read documentation later), the following commands can be used to install Sherpa, depending on your environment and set up.
conda install -c sherpa sherpa
pip install sherpa
python setup.py install
Requirements¶
Sherpa has the following requirements:
- Python 2.7, 3.5, 3.6, or 3.7
- NumPy (the exact lower limit has not been determined, but it is likely to be 1.7.0 or later)
- Linux or OS-X (patches to add Windows support are welcome)
Sherpa can take advantage of the following Python packages if installed:
- astropy: for reading and writing files in FITS format. The minimum required version of astropy is version 1.3, although only versions 2 and higher are used in testing.
- matplotlib: for visualisation of one-dimensional data or models, one- or two- dimensional error analysis, and the results of Monte-Carlo Markov Chain runs. There are no known incompatabilities with matplotlib, but there has only been limited testing. Please report any problems you find.
The Sherpa build can be configured to create the
sherpa.astro.xspec
module, which provides the models and utility
functions from the XSPEC.
The supported versions of XSPEC are 12.10.1 (patch level a or later),
12.10.0, 12.9.1, and 12.9.0.
Interactive display and manipulation of two-dimensional images is available if the DS9 image viewer and the XPA commands are installed. It is expected that any recent version of DS9 can be used.
Releases and version numbers¶
The Sherpa release policy has a major release at the start of the year, corresponding to the code that is released in the previous December as part of the CIAO release, followed by several smaller releases throughout the year.
Information on the Sherpa releases is available from the Zenodo page for Sherpa, using the Digital Object Identifier (DOI) 10.5281/zenodo.593753.
What version of Sherpa is installed?¶
The version number and git commit id of Sherpa can be retrieved from
the sherpa._version
module using the following command:
% python -c 'import sherpa._version; print(sherpa._version.get_versions())'
{'version': '4.10.0', 'full': 'c7732043124b08d5e949b9a95c2eb6833e009421'}
Citing Sherpa¶
Information on citing Sherpa can be found from the CITATION document in the Sherpa repository, or from the Sherpa Zenodo page.
Installing a pre-compiled version of Sherpa¶
Additional useful Python packages include astropy
, matplotlib
,
and ipython-notebook
.
Using the Anaconda python distribution¶
The Chandra X-ray Center provides releases of Sherpa that can be
installed using
Anaconda
from the sherpa
channel. First check
to see what the latest available version is by using:
conda install -c sherpa sherpa --dry-run
and then, if there is a version available and there are no significant upgrades to the dependencies, Sherpa can be installed using:
conda install -c sherpa sherpa
It is strongly suggested that Sherpa is installed into a named conda environment (i.e. not the default environment).
Using pip¶
Sherpa is also available from PyPI at https://pypi.python.org/pypi/sherpa and can be installed with the command:
pip install sherpa
The NumPy package must already have been installed for this to work.
Building from source¶
Prerequisites¶
The prerequisites for building from source are:
- Python versions: 2.7, 3.5, 3.6, 3.7
- Python packages:
setuptools
,numpy
- System:
gcc
,g++
,make
,flex
,bison
(the aim is to support recent versions of these tools; please report problems to the Sherpa issue tracker).
It is highly recommended that matplotlib and astropy be installed before building Sherpa, to avoid skipping a number of tests in the test suite.
The full Sherpa test suite requires the mock package (Python 2.7 only), pytest, and pytest-xvfb. These packages should be installed automatically for you by the test suite if they do not already exist.
Note
As of the Sherpa 4.10.1 release, a Fortran compiler is no-longer required to build Sherpa.
Obtaining the source package¶
The source code can be obtained as a release package from
Zenodo - e.g.
the Sherpa 4.10.0 release -
or from
the Sherpa repository on GitHub,
either a release version,
such as the
4.10.0 tag,
or the master
branch (which is not guaranteed to be stable).
For example:
git clone git://github.com/sherpa/sherpa.git
cd sherpa
git checkout 4.10.0
will use the 4.10.0
tag.
Configuring the build¶
The Sherpa build is controlled by the setup.cfg
file in the
root of the Sherpa source tree. These configuration options
include:
FFTW¶
Sherpa ships with the fftw library source
code and builds it by default. To use a different version, change
the fftw
options in the sherpa_config
section of the
setup.cfg
file. The options to change are:
fftw=local
fftw-include_dirs=/usr/local/include
fftw-lib-dirs=/use/local/lib
fftw-libraries=fftw3
The fftw
option must be set to local
and then the remaining
options changed to match the location of the local installation.
XSPEC¶
Note
The version number of XSPEC must be specified using the
xspec_version
configuration option, as described below. This is
a change from previous releases of Sherpa, but is required in order
to support changes made in XSPEC 12.10.0.
Sherpa can be built to use the Astronomy models provided by
XSPEC versions 12.10.1 (patch level a or later), 12.10.0,
12.9.1, and 12.9.0. To enable XSPEC support, several changes must be
made to the xspec_config
section of the setup.cfg
file. The
available options (with default values) are:
with-xspec = False
xspec_version = 12.9.0
xspec_lib_dirs = None
xspec_include_dirs = None
xspec_libraries = XSFunctions XSModel XSUtil XS
cfitsio_lib_dirs = None
cfitsio_libraries = cfitsio
ccfits_lib_dirs = None
ccfits_libraries = CCfits
wcslib_lib_dirs = None
wcslib_libraries = wcs
gfortran_lib_dirs = None
gfortran_libraries = gfortran
To build the sherpa.astro.xspec
module, the
with-xspec
option must be set to True
and the
xspec_version
option set to the correct version string (the XSPEC
patch level must not be included), and then the
remaining options depend on the version of XSPEC and whether
the XSPEC model library or the full XSPEC system has been installed.
In the examples below, the $HEADAS
value must be replaced
by the actual path to the HEADAS installation, and the versions of
the libraries - such as CCfits_2.5
- may need to be changed to
match the contents of the XSPEC installation.
If the full XSPEC 12.10.1 system has been built then use:
with-xspec = True xspec_version = 12.10.1 xspec_lib_dirs = $HEADAS/lib xspec_include_dirs = $HEADAS/include xspec_libraries = XSFunctions XSUtil XS hdsp_6.25 ccfits_libraries = CCfits_2.5 wcslib_libraries = wcs-5.19.1
where the version numbers were taken from version 6.25 of HEASOFT and may need updating with a newer release.
If the full XSPEC 12.10.0 system has been built then use:
with-xspec = True xspec_version = 12.10.0 xspec_lib_dirs = $HEADAS/lib xspec_include_dirs = $HEADAS/include xspec_libraries = XSFunctions XSModel XSUtil XS hdsp_3.0 ccfits_libraries = CCfits_2.5 wcslib_libraries = wcs-5.16
If the full XSPEC 12.9.x system has been built then use:
with-xspec = True xspec_version = 12.9.1 xspec_lib_dirs = $HEADAS/lib xspec_include_dirs = $HEADAS/include xspec_libraries = XSFunctions XSModel XSUtil XS ccfits_libraries = CCfits_2.5 wcslib_libraries = wcs-5.16
changing
12.9.1
to12.9.0
as appropriate.If the model-only build of XSPEC has been installed, then the configuration is similar, but the library names may not need version numbers and locations, depending on how the
cfitsio
,CCfits
, andwcs
libraries were installed.Note that XSPEC 12.10.0 introduces a new
--enable-xs-models-only
flag when building HEASOFT which simplifies the installation of these extra libraries, but can cause problems for the Sherpa build.
A common problem is to set one or both of the xspec_lib_dirs
and xspec_lib_include
options to the value of $HEADAS
instead of
$HEADAS/lib
and $HEADAS/include
(after expanding out the
environment variable). Doing so will cause the build to fail with
errors about being unable to find various XSPEC libraries such as
XSFunctions
and XSModel
.
The gfortran
options should be adjusted if there are problems
using the XSPEC module.
In order for the XSPEC module to be used from Python, the
HEADAS
environment variable must be set before the
sherpa.astro.xspec
module is imported.
The Sherpa test suite includes an extensive set of tests of this module, but a quick check of an installed version can be made with the following command:
% python -c 'from sherpa.astro import xspec; print(xspec.get_xsversion())'
12.10.1b
Warning
The --enable-xs-models-only
flag with XSPEC 12.10.0 is known
to cause problems for Sherpa. It is strongly recommended that
either that the full XSPEC distribution is built, or that the
XSPEC installation from CIAO 4.11 is used.
Other options¶
The remaining options in the setup.cfg
file allow Sherpa to be
built in specific environments, such as when it is built as part
of the CIAO analysis system. Please
see the comments in the setup.cfg
file for more information on
these options.
Building and Installing¶
Note
It is highly recommended that some form of virtual environment, such as a conda environment or that provided by Virtualenv, be used when building and installing Sherpa.
A standard installation¶
From the root of the Sherpa source tree, Sherpa can be built by saying:
python setup.py build
and installed with one of:
python setup.py install
python setup.py install --user
A development build¶
The develop
option should be used when developing Sherpa (such as
adding new functionality or fixing a bug):
python setup.py develop
Tests can then be run with the test
option:
python setup.py test
The test
command is a wrapper that calls pytest
under the hood,
and includes the develop
command.
You can pass additional arguments to pytest
with the -a
or
--pytest-args
arguments. As an example, a single test can be run
using the syntax:
python setup.py test -a sherpa/astro/datastack/tests/test_datastack.py::test_load::test_case3
Note
If you run both install
and develop
or test
in the same
Python environment you end up with two competing installations of
Sherpa which result in unexpected behavior. If this happens, simply
run pip uninstall sherpa
as many times as necessary, until you
get an error message that no more Sherpa installations are
available. At this point you can re-install Sherpa.
The same issue may occur if you install a Sherpa binary release and then try to build Sherpa from source in the same environment.
The
Sherpa test data suite
can be installed to reduce the number of tests
that are skipped with the following (this is only for those builds
which used git
to access the source code):
git submodule init
git submodule update
When both the DS9 image viewer and XPA toolset are installed, the test suite will include tests that check that DS9 can be used from Sherpa. This causes several copies of the DS9 viewer to be created, which can be distracting, as it can cause loss of mouse focus (depending on how X-windows is set up). This can be avoided by installing the X virtual-frame buffer (Xvfb).
Note
Although the standard Python setuptools approach is used to build
Sherpa, there may be issues when using some of the other build
targets, such as build_ext
. Please report these to the
Sherpa issues page.
Building the documentation¶
Building the documentation requires the Sherpa source code and several additional packages:
- Python 3.5 or greater
- Sphinx, version 1.3 or later
- The
sphinx_rtd_theme
- NumPy, six, and sphinx_astropy
- Graphviz (for the inheritance diagrams)
With these installed, the documentation can be built with the
build_sphinx
target:
python setup.py build_sphinx
This can be done without building Sherpa (either an installation or development version), since Mock objects are used to represent compiled and optional components.
The documentation should be placed in build/sphinx/html/index.html
,
although this may depend on what version of Sphinx is used.
It is also possible to build the documentation from within the docs/
directory:
cd docs
make html
This places the documentation in _build/html/index.html
.
Testing the Sherpa installation¶
A very-brief “smoke” test can be run from the command-line with
the sherpa_smoke
executable:
sherpa_smoke
WARNING: failed to import sherpa.astro.xspec; XSPEC models will not be available
----------------------------------------------------------------------
Ran 7 tests in 0.456s
OK (skipped=5)
or from the Python prompt:
>>> import sherpa
>>> sherpa.smoke()
WARNING: failed to import sherpa.astro.xspec; XSPEC models will not be available
----------------------------------------------------------------------
Ran 7 tests in 0.447s
OK (skipped=5)
This provides basic validation that Sherpa has been installed
correctly, but does not run many functional tests. The screen output
will include additional warning messages if the astropy
or
matplotlib
packages are not installed, or Sherpa was built
without support for the XSPEC model library.
The Sherpa installation also includes the sherpa_test
command-line
tool which will run through the Sherpa test suite (the number of
tests depends on what optional packages are available and how
Sherpa was configured when built):
sherpa_test
The sherpa
Anaconda channel contains the sherpatest
package, which
provides a number of data files in ASCII and FITS formats. This is
only useful when developing Sherpa, since the package is large. It
will automatically be picked up by the sherpa_test
script
once it is installed.